Tissue-specific recombination-activated clonal and inducible transcription (TRAC-IT) enables controlled gene activation in stably marked tissues.

Chemically inducible gene expression systems provide temporal control of transgene activation and therefore represent powerful and widely used tools in plant research. When driven by a cell-type-specific promoter, these systems additionally offer spatial control. However, continued transgene activity is necessarily linked to the preservation of that particular cell type, which might be lost as cells (de)differentiate. To overcome this, we present Tissue-specific Recombination-Activated Clonal and Inducible Transcription (TRAC-IT), a two-step system that uncouples inducible gene expression from cell identity. In the first step, a tissue-specific expressed CRE-GR recombinase is activated upon dexamethasone application, triggering loxP recombination and thereby generating tissue-specific clones of cells expressing YFP and XVE. YFP marks the clone and the XVE trans-activator allows inducible expression of downstream genes within the clone. In the second step, a subsequent β-estradiol application activates XVE to induce transgene expression exclusively within these YFP-marked clones. Because the inducibility of the transgenes becomes genomically anchored, it is maintained upon cell division and/or identity change. TRAC-IT is compatible with Golden Gate cloning, providing simple variation of tissue-specific promoters and transgenes. We show that TRAC-IT supports inducible and controlled tissue-specific clone formation, and that transgenes can be specifically induced within these clones. We employed TRAC-IT to demonstrate that epidermal cells in the root meristem can be persuaded to regenerate somatic embryos through clone-based induction of PLT1 and WOX5. Thus, TRAC-IT offers a versatile tool that provides new technical possibilities to explore the mechanisms driving plant development in a stable tissue-specific fashion.